What are the genomic drivers of the rapid evolution of PRDM9?

Ponting CP. What are the genomic drivers of the rapid evolution of PRDM9? Trends Genet. 2011 Mar 7. [Epub ahead of print] [abstract]
Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.

Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans

Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio GM, et al. (2011) Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans. PLoS ONE 6(3): e17913. doi:10.1371/journal.pone.0017913
Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans. [. . .]

Taking into account only the common hotspots shared by all populations within a given continental region, the proportion of shared hotspots between continental regions is maximum between Europe and Middle East and North Africa (0.52), Europe and Central South Asia (0.44) and between Middle East and North Africa and Central South Asia (0.41). These values are, as expected, much lower when considering Sub-Saharan African or East Asian populations (Table 4). An interesting outcome from this analysis is the number of hotspots common to non African human populations compared to Sub-Saharan Africans. The proportion of hotspots shared between these two groups is only 17.4%, which is a small proportion given the recent out of Africa origin of non African population, and also show that the pace of evolution of hotspots is substantial. Figure S3 shows, as an example, patterns of recombination rates for SNPs where a hotspot event was detected in at least one population. Most variation is observed between continental groups while there is a substantial pattern sharing among populations belonging to the same continental group. [. . .]

Recombination rate appears to be a rapidly changing parameter, indicating that the underlying factors shaping the likelihood of a recombination event, such as DNA sequences controlling recombination rate variation, also change. The change is strongly detectable also in terms of presence or absence of recombination hotspots even if at the present stage it is not possible to measure the relative importance between changes in intermediate recombination rates and the appearing or disappearing of recombination hotspots. This is consistent with recent data showing that allelic variants of PRDM zinc fingers are significantly associated with variability in genome hotspots among humans [8]. The results obtained in this work contribute to the growing perception of recombination not as fixed feature of the genome of a species, but as a phenotype with ample genetic variation.

Elite Afr-Am sprinters more admixed than Afr-Am non-athletes?

Though hardly definitive, this study certainly lends no support to the notion that black dominance of short sprints in the US can be explained purely as a consequence of West African DNA.
The purpose of this study was to compare the mtDNA haplogroup data of elite groups of Jamaican and African-American sprinters against respective controls to assess any differences in maternal lineage. The first hypervariable region of mtDNA was haplogrouped in elite Jamaican athletes (N=107) and Jamaican controls (N=293), and elite African-American athletes (N=119) and African-American controls (N=1148). Exact tests of total population differentiation were performed on total haplogroup frequencies. The frequency of non-sub-Saharan haplogroups in Jamaican athletes and Jamaican controls was similar (1.87% and 1.71%, respectively) and lower than that of African-American athletes and African-American controls (21.01% and 8.19%, respectively). There was no significant difference in total haplogroup frequencies between Jamaican athletes and Jamaican controls (P=0.551 ± 0.005); however, there was a highly significant difference between African-American athletes and African-American controls (P<0.001). The finding of statistically similar mtDNA haplogroup distributions in Jamaican athletes and Jamaican controls suggests that elite Jamaican sprinters are derived from the same source population and there is neither population stratification nor isolation for sprint performance. The significant difference between African-American sprinters and African-American controls suggests that the maternal admixture may play a role in sprint performance.
[. . .]
Among African Americans, no individual haplogroup produced significant findings for Bonferroni-adjusted critical a of 0.003, presented in Table 3. Interestingly, the nonsub- Saharan paragroup was highly significant in overrepresentation within athletes. This may indicate an advantage possessed by more admixed individuals. While maternal admixture contributing any environmental and social advantages with regard to athletic training and development cannot be ruled out, further investigation into the amount of admixture in the autosomal genome is required to assess the overall non-African genomic component. In addition to assessing differences between athletes and controls in either group, the haplogroup distributions of Jamaican controls and African-American controls were also compared. These two populations were found to have significantly different haplogroup distributions (Po0.001), providing further mitochondrial evidence of different population histories. The matrilineal distribution of both athlete populations differs significantly, suggesting no discernable distribution of lineages indicative of elite sprinting in these genetically distinct groups of West African descent.
Reference: Deason et al. Scand J Med Sci Sports. 2011 Mar 16. doi: 10.1111/j.1600-0838.2010.01289.x. [Epub ahead of print]

Ethnic background of the British Royal family

From the website of genealogist William Addams Reitwiesner, who died last year. The Ethnic ancestry of Prince William (b. 1982):
Every so often, someone will state that the British Royal Family is "not British", that they are instead "German" or "Foreign". Since this belief seems to be somewhat wide-spread, and since the genealogy of many members of the British Royal Family is fairly well known, it seemed to me that it would be fairly easy to quantify precisely how "British" or "non-British" the British Royal Family is. This webpage shows the results of my work.

A few links

The Unsilenced Science: The Racial Controversy of a Violent Gene

Viking ancestry explored on the Isle of Man by researchers
Viking's first took up settlement on the Isle of Man at the end of the 8th century.

The research team will analyse Y chromosomes which are linked with surnames and then estimate proportions of Norwegian ancestry in these samples.

Recent adverse trends in semen quality and testis cancer incidence among Finnish men
These simultaneous and rapidly occurring adverse trends suggest that the underlying causes are environmental and, as such, preventable. Our findings necessitate not only further surveillance of male reproductive health but also research to detect and remove the underlying factors.

Genetic Genealogy and the Single Segment. One minor point of disagreement. The author writes:
What this means for genealogy on 23andMe is that for two people sharing one segment identical by descent there is no way to reliably estimate how far back the common ancestor was. Furthermore, no improvement in software can possibly change that, because the limitation is imposed by the genetics itself.
For relatively sparse databases and at present levels of testing resolution, this is more or less true. However, two things could potentially change this: (1) denser databases linked to pedigree information should allow small segments in living individuals to be attributed with high confidence to particular distant ancestors in many cases; (2) high-quality complete genome sequences should provide additional resolution, potentially allowing the level of relationship represented by a small segment to be estimated with greater precision (e.g. using STR haplotypes, recent/novel SNPs, and other sorts of variation not captured by SNP microarrays).